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| CGHbase-package | CGHbase: Base functions and classes for arrayCGH data analysis. |
| avedist | Retrieve regions information from cghRegions object. |
| avedist,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data. |
| bpend | Retrieve feature position data from cgh objects. |
| bpend,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| bpend,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| bpend,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data. |
| bpend,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| bpstart | Retrieve feature position data from cgh objects. |
| bpstart,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| bpstart,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| bpstart,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data. |
| bpstart,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| calls | Retrieve copynumber data from cgh objects. |
| calls,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| calls<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data. |
| CGHbase | CGHbase: Base functions and classes for arrayCGH data analysis. |
| cghCall | Class to contain and describe called array comparative genomic hybridization data. |
| cghCall-class | Class to contain and describe called array comparative genomic hybridization data. |
| cghRaw | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| cghRaw-class | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| cghRegions | Class to contain and describe array comparative genomic hybridization regions data. |
| cghRegions-class | Class to contain and describe array comparative genomic hybridization regions data. |
| cghSeg | Class to contain and describe segmented array comparative genomic hybridization data. |
| cghSeg-class | Class to contain and describe segmented array comparative genomic hybridization data. |
| chromosomes | Retrieve feature position data from cgh objects. |
| chromosomes,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| chromosomes,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| chromosomes,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data. |
| chromosomes,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| class:cghCall | Class to contain and describe called array comparative genomic hybridization data. |
| class:cghRaw | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| class:cghRegions | Class to contain and describe array comparative genomic hybridization regions data. |
| class:cghSeg | Class to contain and describe segmented array comparative genomic hybridization data. |
| copynumber | Retrieve copynumber data from cgh objects. |
| copynumber,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| copynumber,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| copynumber,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| copynumber<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data. |
| copynumber<-,cghRaw,matrix-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| copynumber<-,cghSeg,matrix-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| frequencyPlot | Visualization of aCGH regions. |
| frequencyPlot,cghRegions,missing-method | Class to contain and describe array comparative genomic hybridization regions data. |
| initialize,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| initialize,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| initialize,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data. |
| initialize,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| nclone | Retrieve regions information from cghRegions object. |
| nclone,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data. |
| plot.cghCall | Plot aCGH data. |
| plot.cghCall,cghCall,missing-method | Class to contain and describe called array comparative genomic hybridization data. |
| plot.cghRaw | Plot aCGH data. |
| plot.cghRaw,cghRaw,missing-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| plot.cghRegions | Plot aCGH data. |
| plot.cghRegions,cghRegions,missing-method | Class to contain and describe array comparative genomic hybridization regions data. |
| plot.cghSeg | Plot aCGH data. |
| plot.cghSeg,cghSeg,missing-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| probamp | Retrieve call probabilities from a cghCall object. |
| probamp,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| probamp<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data. |
| probgain | Retrieve call probabilities from a cghCall object. |
| probgain,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| probgain<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data. |
| probloss | Retrieve call probabilities from a cghCall object. |
| probloss,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| probloss<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data. |
| probnorm | Retrieve call probabilities from a cghCall object. |
| probnorm,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| probnorm<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data. |
| regions | Retrieve regions data from cghRegions object. |
| regions,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data. |
| regions<-,cghRegions,matrix-method | Class to contain and describe array comparative genomic hybridization regions data. |
| segmented | Retrieve copynumber data from cgh objects. |
| segmented,cghCall-method | Class to contain and describe called array comparative genomic hybridization data. |
| segmented,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| segmented<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data. |
| segmented<-,cghSeg,matrix-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| summaryPlot | Visualization of aCGH profiles. |
| summaryPlot,cghCall,missing-method | Class to contain and describe called array comparative genomic hybridization data. |
| WiltingCalled | Cervical cancer arrayCGH data called with CGHcall |
| WiltingData | Cervical cancer arrayCGH data |
| WiltingNorm | Normalized log2 ratios from cervical cancer arrayCGH data. |
| WiltingRaw | Raw log2 ratios from cervical cancer arrayCGH data. |
| WiltingRegions | Regions of cervical cancer arrayCGH data as defined by CGHregions |
| WiltingSeg | Segmented log2 ratios from cervical cancer arrayCGH data. |